Barley RNA viromes in six different geographical regions in Korea

Yeonhwa Jo,Won Kyong Cho,Ju-Young Bae,Bong Choon Lee,Sang-Min Kim,Hoseong Choi

doi:10.1038/s41598-018-31671-4

Yeonhwa Jo, Won Kyong Cho + Show 4 more

Open Access

https://doi.org/10.1038/s41598-018-31671-4

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Abstract

Barley is a kind of cereal grass belonging to the family Poaceae. To examine viruses infecting winter barley in Korea, we carried out a comprehensive study of barley RNA viromes using next-generation sequencing (NGS). A total of 110 barley leaf samples from 17 geographical locations were collected. NGS followed by extensive bioinformatics analyses revealed six different barley viromes: Barley yellow mosaic virus (BaYMV), Barley mild mosaic virus (BaMMV), Barley yellow dwarf virus (BYDV), Hordeum vulgare endornavirus (HvEV), and Barley virus G (BVG). BaYMV and HvEV were identified in all libraries, while other viruses were identified in some specific library. Based on the number of virus-associated reads, BaYMV was a dominant virus infecting winter barley in Korea causing yellow disease symptoms. We obtained nearly complete genomes of six BaYMV isolates and two BaMMV isolates. Phylogenetic analyses indicate that BaYMV and BaMMV were largely grouped based on geographical regions such as Asia and Europe. Single nucleotide polymorphisms analyses suggested that most BaYMV and BaMMV showed strong genetic variations; however, BaYMV isolate Jeonju and BaMMV isolate Gunsan exhibited a few and no SNPs, respectively, suggesting low level of genetic variation. Taken together, this is the first study of barley RNA viromes in Korea.

Highlights

Barley (Hordeum vulgare L.) is a kind of cereal grass belonging to the family Poaceae
DsRNA extraction followed by next-generation sequencing (NGS) was used to determine the complete genome sequences of Hordeum vulgare endornavirus (HvEV), which is composed of dsRNA23
As compared to the previous studies associated with viruses infecting barley, our study focuses on barley RNA viromes associated with identification of viruses infecting barley, as well as geographical distribution and genetic diversity of identified viruses in Korea

Summary

Introduction

Barley (Hordeum vulgare L.) is a kind of cereal grass belonging to the family Poaceae. Complete genome sequence of Barley yellow striate mosaic virus (BYSMV) in the genus Cytorhabdovirus was assembled by small RNA sequencing followed by Sanger-sequencing[24]. The contigs obtained by Trinity and Velvet as well as raw sequence reads in each library were blasted against a viral reference database to identify viruses infecting barley.

Results

Conclusion